library_size_normalisation: performs a whole library size normalisation of the selected...

In TeamMacLean/atacr: Analysing Capture Seq Count Data

Description

performs a whole library size normalisation of the selected set of windows, calculates a median virtual experiment and normalises to that

Usage

library_size_normalisation(data, which = "bait_windows",
  by_treatment = FALSE)

Arguments

data	a list of SummarizedExperiment objects from atacr::make_counts()
which	the subdivision of the genome to calculate correlations either 'whole_genome', 'bait_windows' or 'non_bait_windows'
by_treatment	(FALSE) will group the assay into different treatments and normalise each separately - assumes that within treatment groups the samples should show little difference, but between sample treatment groups could show lots of difference between windows.

Value

a SummarizedExperiment object with a new, normalised assay matrix

TeamMacLean/atacr documentation built on May 9, 2019, 4:24 p.m.